Forum Topic: How to match the blast Nicotiana gene to its expression data
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How to match the blast Nicotiana gene to its expression data
Dear all, I would like to know how to match the blast Nicotiana gene to its expression data? I have downloaded the microarray data of tobacco gene expression from the EMBL-EBI ArrayExpress. At the same time, I blast my intsrested gene from N.tabacum TN90. It showed the related information (mRNA_60941 gene_35596|id=AT2G19450.1:evalue=0.0:annot='membrane bound O-acyl transferase (MBOAT) family protein';id=Solyc12g008970.1.1:evalue=0.0:annot='Diacylglycerol acyltransferase'Length=1524). But how can I match the blast information to the ID in expression data? I searched a lot but I couldn't find it. Please help. Thank you very much.
This topic was started by Xun Weng.
Dear all, I would like to know how to match the blast Nicotiana gene to its expression data? I have downloaded the microarray data of tobacco gene expression from the EMBL-EBI ArrayExpress. At the same time, I blast my intsrested gene from N.tabacum TN90. It showed the related information (mRNA_60941 gene_35596|id=AT2G19450.1:evalue=0.0:annot='membrane bound O-acyl transferase (MBOAT) family protein';id=Solyc12g008970.1.1:evalue=0.0:annot='Diacylglycerol acyltransferase'Length=1524). But how can I match the blast information to the ID in expression data? I searched a lot but I couldn't find it. Please help. Thank you very much.
This topic was started by Xun Weng.
Posted by adam Stein on 2025-02-15 01:27:53
Matching your BLAST-identified Nicotiana gene to its expression data from the ArrayExpress microarray dataset involves several steps:
### 1. **Understand the BLAST Output**
- Your BLAST results give a match for your query sequence to a reference genome (N. tabacum TN90).
- You obtained an identifier like `mRNA_60941 gene_35596`, which may be specific to the genome annotation.
- The result also includes homology to Arabidopsis (`AT2G19450.1`) and tomato (`Solyc12g008970.1.1`).
### 2. **Check the Microarray Data Format**
- Open the expression data file from ArrayExpress (often in TXT or CSV format).
- Look for the gene identifier format (e.g., Gene ID, Probe ID, or transcript ID).
- Expression data typically uses **probe IDs** or **gene symbols**, which need to be mapped to genome annotations.
### 3. **Find Corresponding IDs**
- Look up **gene annotations for N. tabacum TN90** to map `mRNA_60941` or `gene_35596` to a standard identifier.
- Possible sources:
- **Sol Genomics Network (SGN)**: [https://solgenomics.net/](https://solgenomics.net/)
- **Tobacco Genome Hub**: [https://www.ncbi.nlm.nih.gov/genome/12449](https://www.ncbi.nlm.nih.gov/genome/12449)
- **Ensembl Plants**: [https://plants.ensembl.org/Nicotiana_tabacum/Info/Index](https://plants.ensembl.org/Nicotiana_tabacum/Info/Index)
- Search for your BLAST-matched gene and find its corresponding **Gene ID or Probe ID**.
### 4. **Map to Expression Data**
- Once you identify the standard Gene ID for your gene, match it with the **ID column** in the microarray dataset.
- If the microarray data uses **probe IDs**, you may need a probe-to-gene mapping file, which is often available in ArrayExpress or GEO (Gene Expression Omnibus).
### 5. **Alternative Approach: Functional Homology**
- If the exact gene ID is missing in the expression dataset, look for homologous genes (e.g., the Arabidopsis `AT2G19450.1` or tomato `Solyc12g008970.1.1`).
- Check whether the dataset includes functional annotations or gene ontology (GO) terms to find a related gene.
If you're still having trouble, try providing the **ArrayExpress accession number** so I can help you find specific mapping files.
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### 1. **Understand the BLAST Output**
- Your BLAST results give a match for your query sequence to a reference genome (N. tabacum TN90).
- You obtained an identifier like `mRNA_60941 gene_35596`, which may be specific to the genome annotation.
- The result also includes homology to Arabidopsis (`AT2G19450.1`) and tomato (`Solyc12g008970.1.1`).
### 2. **Check the Microarray Data Format**
- Open the expression data file from ArrayExpress (often in TXT or CSV format).
- Look for the gene identifier format (e.g., Gene ID, Probe ID, or transcript ID).
- Expression data typically uses **probe IDs** or **gene symbols**, which need to be mapped to genome annotations.
### 3. **Find Corresponding IDs**
- Look up **gene annotations for N. tabacum TN90** to map `mRNA_60941` or `gene_35596` to a standard identifier.
- Possible sources:
- **Sol Genomics Network (SGN)**: [https://solgenomics.net/](https://solgenomics.net/)
- **Tobacco Genome Hub**: [https://www.ncbi.nlm.nih.gov/genome/12449](https://www.ncbi.nlm.nih.gov/genome/12449)
- **Ensembl Plants**: [https://plants.ensembl.org/Nicotiana_tabacum/Info/Index](https://plants.ensembl.org/Nicotiana_tabacum/Info/Index)
- Search for your BLAST-matched gene and find its corresponding **Gene ID or Probe ID**.
### 4. **Map to Expression Data**
- Once you identify the standard Gene ID for your gene, match it with the **ID column** in the microarray dataset.
- If the microarray data uses **probe IDs**, you may need a probe-to-gene mapping file, which is often available in ArrayExpress or GEO (Gene Expression Omnibus).
### 5. **Alternative Approach: Functional Homology**
- If the exact gene ID is missing in the expression dataset, look for homologous genes (e.g., the Arabidopsis `AT2G19450.1` or tomato `Solyc12g008970.1.1`).
- Check whether the dataset includes functional annotations or gene ontology (GO) terms to find a related gene.
If you're still having trouble, try providing the **ArrayExpress accession number** so I can help you find specific mapping files.
https://troubleshoot.dev https://latestmerch.com https://programable.com https://attorney.work/ https://authenticjerseysstore.com/
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